33- Novoa T, Laplaza R, Peccati F, Fuster F, Contreras-García J. The NCIWEB Server: "A Novel Implementation of the Noncovalent Interactions Index for Biomolecular Systems", Journal of chemical information and modeling, 2023 Aug 14;63(15):4483-4489. https://pubs.acs.org/doi/10.1021/acs.jcim.3c00271.
It is well-known that the activity and function of proteins is strictly correlated with their secondary, tertiary, and quaternary structures. Their biological role is regulated by their conformational flexibility and global fold, which, in turn, is largely governed by complex noncovalent interaction networks. Because of the large size of proteins, the analysis of their noncovalent interaction networks is challenging, but can provide insights into the energetics of conformational changes or protein-protein and protein-ligand interactions. The noncovalent interaction (NCI) index, based on the reduced density gradient, is a well-established tool for the detection of weak contacts in biological systems. In this work, we present a web-based application to expand the use of this index to proteins, which only requires a molecular structure as input and provides a mapping of the number, type, and strength of noncovalent interactions.
32- R. Laplaza; J. Contreras-Garcia; F. Fuster; F. Volatron; P. Chaquin "Dependence of hydrocarbon sigma CC bond strength on bond angles: the concepts of "inverted", "direct" and "superdirect" bonds", Computational and Theoretical Chemistry, volume 1207, January 2022, article 113505., https://doi.org/10.1016/j.comptc.2021.113505.
The bond energy (BE) of CC in CH3-CH3 with respect to geometry frozen fragments follows a sigmoidal increase as a function of the θ = HCC pyramidalization angle. Using dynamic orbital forces as a BE index, the same behaviour as a function of a unique <θ> parameter, mean angle of the substituents, is found for 24 single CC bonds in various hydrocarbons. Thus the <θ> parameter appears as a straightforward and robust index of the geometrical constraints which can either strengthen or weaken a bond. This way, CC sigma bonds can be easily classified into weak “inverted” bonds for <θ> < 90° (eg. in [111]propellane and bicyclobutane), “direct” (or “normal”) bonds for 90° < <θ> < 120° (eg. ethane), and strong “superdirect” bonds for <θ> > 120° (eg. in tetrahedryl-tetrahedrane and butadiyne).
31- Laplaza R, Contreras-García J, Fuster F, Volatron François, Chaquin P. From “inverted” to “superdirect“ bonds: a general concept connecting substituent angles with sigma bond strengths. The case of the CC bonds in hydrocarbons. ChemRxiv. Cambridge: Cambridge Open Engage; 2021.https://chemrxiv.org/engage/chemrxiv/article-details/60d97aaa261611396a8c9bde
The C-C bond energy with respect to geometry frozen fragments (BE) has been calculated for C2H6 as a function of θ = H-C-C angles. BE decreases rapidly when θ decreases from its equilibrium value to yield the so-called “inverted bonds” for θ < 90°; on the contrary BE increases with θ to yield somehow “superdirect” bonds, following a sigmoidal variation related to orbital overlap. The central bonds in Si2H6, Ge2H6 and N2H4 as well as the C-H bond in CH3-H behave similarly. The concept of “invertedness”/”directedness” is generalized to any CC sigma bond in hydrocarbons and characterized by the mean angle value <θ> of substituents. Using dynamic orbital forces (DOF) as indices, the intrinsic sigma bond energies are studied as a function of <θ> for 24 formally single bonds in a panel of 22 molecules. BE decreases from the strongest “superdirect” bonds in butadiyne, (<θ> = 180°) or tetrahedrylacetylene to the weakest “inverted bonds” in cyclobutene, tetrahedrane, bicyclobutane and [1.1.1]propellane (<θ> = 60°), following a sigmoidal variation.
30- P. Chaquin, F. Volatron, F. Fuster, "Définir le caractère liant/antiliant d’une orbitale moléculaire : de l'amphi à la recherche", l'Actualité Chimique, 2020, 447, 28-37.
Qualifier une orbitale moléculaire (OM) de liante, antiliante ou non liante est un exercice familier à tout enseignant
de chimie des premières années d’enseignement supérieur. Ces notions sont faciles à mettre en œuvre et très
fécondes en ce qui concerne de nombreuses propriétés telles que les longueurs de liaison, l’état de spin, etc.
Malheureusement, elles deviennent nettement plus difficiles à définir au plan quantitatif et même au plan qualitatif
lorsque l’on cherche à calculer précisément les OM. Le but de cet article est de faire un tour d’horizon de ces notions
telles qu’elles sont utilisées en cours et de les approfondir en les reliant aux forces exercées par les électrons sur
les noyaux. Le calcul de ces « forces orbitalaires » est actuellement utilisé en recherche, notamment pour l’étude
de liaisons « exotiques » comme dans le propellane, exemple abordé en conclusion.
29- F. Fuster & P. Chaquin. "Analysis of carbon-carbon bonding in small hydrocarbons and dicarbon using dynamic orbital forces : Bond energies and sigma-pi partition. Comparison with sila compounds.", Int. J. Quant. Chem., 2019, 119(20).
The CC bonding is analyzed using dynamic orbital forces (DOF) in the series cyclopropane‐ethane‐ benzene‐ethylene‐acetylene. The sum Σ(DOF)t of the DOF over occupied molecular orbitals (MOs) is found linearly correlated to bond energies and thus can be used as a tool for determination of CC bond strength. A partition of bonding into σ and π components indicates a weakening of the σ bonding along the series, mainly due to the decrease of the bonding character of the highest σ MO. For C2 molecule, Σ(DOF) t was computed taking into account the four dominant configurations. On the basis of the preceding correlation, the C2 bond was found about 15 kcal/mol weaker than that of acetylene, with a 25% σ participation; the bond order of C2 can be evaluated at about 2.8 if we assume bond orders of 3 for acetylene and 2 for ethylene. Some sila homologs of the preceding carbon compounds have been studied. They exhibit characteristics generally close to the carbon compounds. A quite good correlation between Σ(DOF)t and bond energies is also observed.28- R. Laplaza, J. Contreras-Garcia, F. Fuster, F. Volatron, P. Chaquin, "The ‘inverted Bonds’ revisited. Analysis of ‘in silico’ models and of [1.1.1]Propellane using Orbital Forces", Chem. Eur. J., 2019, 26(30), p. 6839-6845..
This article dwells on the nature of “inverted bonds”, which make reference to the s interaction between two s‐p hybrids by their smaller lobes, and their presence in [1.1.1]propellane 1 . Firstly we study H 3 C‐C models of C‐C bonds with frozen HCC angles reproducing the constraints of various degrees of “inversion”. Secondly, the molecular orbital (MO) properties of [1.1.1]propellane 1 and [1.1.1]bicyclopentane 2 are analyzed with the help of orbital forces as a criterion of bonding/antibonding character and as a basis to evaluate bond energies.
27- F. Chemla , F. Fuster , H. Gérard , A. Markovits , A. Naitabdi , R. Vuilleumier, "Un laboratoire pédagogique à grande échelle : les ateliers bidisciplinaires", l'Actualité
Chimique, Société Française de Chimie, octobre 2018, 433.
Un enseignement bidisciplinaire obligatoire a été mis en place en première année de licence, basé sur la réalisation en petits groupes de projets en autonomie partielle. Ces « ateliers » sont centrés sur l’acquisition des compétences liées à l’initiation à la recherche : auto-apprentissage, construction et mise en place d’une démarche d’investigation scientifique, présentation des résultats et justification/défense des choix et conclusions présentées.
26- P. Chaquin, F. Fuster et F. Volatron, "Bonding/antibonding character of “lone pair” molecular orbitals from their energyderivatives; consequences for experimental data.", Int J Quantum Chem. 2018, 118, 1-12.
The derivative of molecular orbitals (MO) energies with respect to a bond length (dynamic orbital force [DOF]) is used to estimate the bonding/antibonding character of valence MOs along thisbond, with a focus on lone pair MOs, in a series of small molecules: AH (A = F, Cl, Br), AH2(A = O, S, Se), AX3 (A = N, P, As; X = H, F), and H2CO. The HOMO DOF agrees with the calculated varia-tion of bond length and force constant in the corresponding ground state cation, and of bondlength variation by protonation. These results also agree with available experimental data. It is worthy to note that the p-type HOMOs in AH and AH2 are found bonding. The lone pair MO isbonding in NH3, while it is antibonding in PH3, AsH3, and AF3.
25- P. Chaquin, F. Fuster et F. Volatron, "Apprendre la chimie avec les orbitales - OrbiMol, une boîte à outils pédagogique ", Union des professeurs de physique et de chimie, 2018, 112, 1-12. Article invité pour le 1000e numéro.
Dans une première partie, nous en rappellerons les caractéristiques utiles en lien avec des propriétés physico-chimiques observables ; puis nous présenterons la base de données OrbiMol. Ensuite, nous montrerons quelques exemples classiques ou moins connus d’exploitation de ces données.
24- P. Chaquin and F. Fuster, "Analysis of Reaction Processes based on the Evolution of Dynamic Orbital Force (DOF); Examples of Cycloadditions, SN2 Substitution, nucleophilic Addition and Hydrogen Transposition", ChemPhysChem, 2017, 18, 1-9.
The study of the dynamic orbital forces (DOF), determining the MO bonding/antibonding character on selected bonds (or other geometrical parameter), along a RC allows a deeper insight on reaction processes. It highlights the nature of the main MO reorganizations, and at what stage of the RC they occur. For instance, in the Diels-Alder reaction, it is possible to identify a part of the reaction dominated by repulsive 4-electron interaction and a part dominated by attractive 2-electron interactions. Also, the shape of the DOFs as a function of the RC reveals the existence of avoided MO crossings and their precise location. Even in spontaneous reactions with a monotonous potential energy variation, like the addition of hydride ion to carbonyl, extremums of MO energy and sudden electron rearrangements can be put in evidence.
23- E. Alikhani, F. Fuster, B. Madebene, S. J. Grabowski, "Topological Reaction Sites - Very Strong Chalcogen Bonds", Physical Chemistry Chemical Physics, 2014,16, 2430-2442.
The analysis of interactions in complexes of S(CN)2, Se(CN)2, SFCl and SeFCl with F- and Cl- anions is performed here. The sulphur and selenium atoms act in these complexes as Lewis acid centres interacting with fluorine and chlorine anions. The arrangement of sub-units in complexes is in agreement with the σ-hole concept; particularly it is a result of contacts between positive and negative electrostatic potentials´ sites. The interactions in complexes analyzed may be classified as very strong charge assisted chalcogen bonds and they possess numerous characteristics typical for covalent bonds. Even in a case of complexes of SFCl and SeFCl, i.e. SFCl2- and SeFCl2-, the trivalency of the chalcogen atom is observed. The calculations were carried out at the MP2(full)/aug-cc-pVTZ level of approximation, the analyses were performed with the use of the Natural Bond Orbital (NBO) method, the Quantum Theory of ´Atoms in Molecules´ (QTAIM) and the Electron Localization Function (ELF) approach. The results obtained by these methods are in agreement giving the consistent picture of the complexes´ configurations and the electron charge distribution for them. The QTAIM and ELF approaches allow to predict for S(CN)2, Se(CN)2, SFCl and SeFCl molecules the directions of nucleophilic attack. They are in line with the prediction based on the σ-hole concept. The Symmetry Adapted Perturbation Theory (SAPT) approach was applied to deepen the understanding of the nature of interactions.
22- P. Chaquin et F. Fuster, “Enseigner la Chimie
Organique avec les orbitales. Présentation d’une base de données d’orbitales
moléculaires”, l'Actualité
Chimique, 369, 2012.
Version électronique ici
Nous souhaitons par cet article inciter à une
utilisation des orbitales moléculaires dans l’enseignement de la Chimie
Organique dès la deuxième, voire la première année de l’enseignement supérieur.
Pour cela, on propose des pré-requis évitant tout développement mathématique.
Puis on présente une base en ligne, récemment créée, d’orbitales moléculaires
adaptées à cet enseignement. Enfin, on montre sur quelques exemples comment ces
données peuvent être exploitées pour expliquer des mécanismes réactionnels de
base.
We wish in this paper
to prompt educators in Organic Chemistry to use molecular orbitals as soon as
possible. For this purpose, we first propose a set of preliminary concepts
which does not involve any mathematical features. Then we present a molecular
orbital database containing nearly 250 molecules especially designed for
chemical education. Finally, we show how these data could be used to clear up
some selected basic reaction mechanisms.
21- Franck Fuster and Slawomir Grabowski “Intramolecular Hydrogen Bonds: the QTAIM and ELF
Characteristics”, Journal of Physical Chemistry A (2011), 115(35), 10078–10086.
B3LYP/aug-cc-pVTZ calculations were
performed on the species with intramolecular O–H···O hydrogen bonds. The
Quantum Theory of Atoms in Molecules (QTAIM) and the Electron Localization
Function (ELF) method were applied to analyze these interactions. Numerous
relationships between ELF and QTAIM parameters were found. It is interesting
that the CVB index based on the ELF method as well as the total electron energy
density at the bond critical point of the proton–acceptor distance (Hbcp) may
be treated as universal descriptors of the hydrogen bond strength, they are
also useful to estimate the covalent character of this interaction. There are
so-called resonance-assisted hydrogen bonds (RAHBs) among the species analyzed
here. It was found that there are not any distinct differences between RAHBs
and the other intramolecular hydrogen bonds.
20- Fernandez,
Sebastien; Markovits, Alexis; Fuster, Franck; Minot, Christian, “First Row
Transition Metal Atom Adsorption on Defect-Free MgO(100) Surface”, Journal
of Physical Chemistry C (2007), 111(18), 6781-6788.
Periodic d. functional calcns. were used
for a systematic study of the adsorption of metal atoms on the MgO(100)
surface. The complete period of Mendeleev's table, M = K to Zn, was
considered. The evolution of the adsorption energies, along this series, is
similar to that of the cohesive energies of the pure metals, showing 2 maxima
for Ti and Ni. The origin of this behavior was discussed, showing that, at
high coverage, the M-M interaction contributes to this trend. However, it is
also found at low coverage when M-M interactions are negligible. The
adsorption energy then results from 2 main interactions between M and the
surface. That with Osurf is the dominant one, and the position on top of the
Osurf position is always the most stable adsorption mode. Such interaction
also leads to an energy curve presenting 2 maxima for Ti and Ni. A similar
trend could be generalized to cases where M interacts with other bases than
Osurf. The interaction of M with the Mgsurf adjacent to the adsorption site
should also be taken into account when M is large (M = K to V). The MO anal.
of these interactions is supported by the presentation of the projected d. of
states.
19- Philippe
Soler, Jacqueline Bergès, Franck Fuster, Hilaire Chevreau, “Dynamical
hydrogen-induced electronic relocalization in S2H2 and S2H2-“, Chemical Physics Letters, (2005), Volume
411, Issues 1-3, , Pages 117-12.
A time-dependent topological analysis of
the electron the electron relocalization processes in S2H2 and S2H2- shows that
topol. charge and spin relocalization processes can be related to the hydrogen
motions, and questions the role of hydrogen vibrations in complement to
possible hydrogen bonds in biol. systems.
18- Alikhani, M.
E.; Fuster, F.; Silvi, B; “What Can Tell the Topological Analysis of ELF on
Hydrogen Bonding? “, Structural Chemistry (2005), 16(3), 203-210.
A review. The topol. anal. of the electron
localization function (ELF) provides a convenient math. framework enabling an
unambiguous characterization of bonds, and more particularly in terms of bond
types. In this communication we present an overview of the application of this
approach to hydrogen bonding in which we attempt to answer the following
questions: 1. What is the ELF based topol. definition of the hydrogen bond; 2.
Is a hydrogen bonded complex a mol. or an assembly of mols.; 3. Is there a
topol. descriptor of the hydrogen bond strength; 4. Is it possible to provide a
sub-classification of hydrogen bonds; 5.Is the topol. approach predictive of
the structure of the complex.
17- Soler,
Philippe; Fuster, Franck; Chevreau, Hilaire, “Fast topological analysis of 2D
and 3D grids of data: Application to the Atoms in Molecule (AIM) and the
Electron Localization Function (ELF)”, Journal of Computational Chemistry
(2004), 25(15), 1920-1925.
The topological analysis of grids of data
is used for detn. of surfaces or vols. around maxima. The vols. are then
related to chem. information such as atoms or bonds, and can be used for
integration of local properties such as electronic population. The problem of
global connectivity is reversed into the question of local connectivity
yielding a linear scaling partition algorithm. Two packages are developed for
a very fast anal. and partition of 2-dimensional or 3-dimensional grids of
data, applications being made to C2H2, C2H4, C6H6, H2CO, and H2CS mols. using
the Atoms in Mol. (AIM) or Electron Localization Function (ELF).
16- Fuster,
Franck; Dezarnaud-Dandine, Christine; Chevreau, Hilaire; Sevin, Alain, “A
theoretical study of the bonding in NO, (NO)2, (NO)2- and (NO)22- using a
topological analysis of the electron localization function”, Physical
Chemistry Chemical Physics (2004), 6(13), 3228-3234.
The topol. anal. of the ELF function calcd.
at the DFT level for (NO)2, (NO)2- and (NO)22- reveals a regular variation in
the NN bonding. In the neutral species, a very weak attraction results form
the fluctuation of a small electron population assocd. with the N lone pairs.
A similar but even weaker attraction is found between the O atoms, thus
favoring the cis geometry. The same trends are found in the cis anion,
although in the more stable trans isomer a NN bonding basin appears. The
latter bonding basin is more pronounced in the dianions. The MO localization
function (MOLF) method which is briefly described, is proposed for gaining
information on the σ/π sepn.
15- Silvi, B.;
Pilme, J.; Fuster, F.; Alikhani, M. E. “What can tell topological approaches on
the bonding in transition metal compounds”, NATO Science Series, II:
Mathematics, Physics and Chemistry (2003), 116(Metal-Ligand Interactions),
241-284.
A review. The bonding in mols. contg.
transition metal atoms is generally described and explained by model based on
orbitals. Alternatively, topol. approaches such as the Atoms in Mols. (AIM)
theory or the Electron Localization function (ELF) anal. offer an orbital
independent framework enabling the partition of the mol. position space into
basins of attractors bearing a chem. signification. It is then possible to
recover familiar chem. objects such as atoms, bonds and lone pairs. We present
an overview of the possibility offered by the ELF anal. to investigate the
bonding in the transition metal compds. ranging from isolated atoms to solids.
The M-shell population of the ground state atoms is always less than the
expectation (Z-12 or Z-11) whereas that of the N-shell is greater than 2 or 1
in the case of Cr and Cu. The bonding in the TM di and tri-halides has been
investigated and it shown that the populations in the MF3 series (M = Sc, ...,
Zn) can be rationalized by invoking the contribution of resonance structures in
which the fluorine atom forms a dative bond with the metal and therefore does
not fulfil the octet rule. The bonding in carbonyl complexes is mostly
characterized by the population and the spin d. population of the V(C, M) basin
which accepts most of the net d. transfers from the metal whereas the sum of
the populations of the remaining carbonyl moiety-remains almost equal to that
calcd. in free carbon monoxide. In bimetallic complexes, such as M2(HNCHNH)4
(M = Nb, ..., Pd) our anal. shows that there is a huge delocalization between
the two metallic subunit which is revealed by the value of the variance of the
corresponding populations. This delocalization appears to be a direct
consequence of the symmetry and of diamagnetism of these mols. In all these
examples, the localization of the spin d. is a clue to interpret the bonding.
Examples of multicenter bonds favored by the size of the transition metallic
cores are presented which shed light onto the nature of agostic hydrogen
interaction as well as on planar tetracoordinated carbons and of bulk metals.
Results concerning chemisorption on a catalyst surface and the bonding in bulk
metal oxides are discussed.
14- Silvi,
Bernard; Kryachko, Eugene S.; Tishchenko, Oksana; Fuster, Franck; Nguyen, Minh
Tho, “Key properties of monohalogen substituted phenols: interpretation in
terms of the electron localization function”, Molecular Physics (2002),
100(11), 1659-1675.
This paper is an attempt to bridge the key
properties of monohalogen substituted phenols with the electronic localization
function, which has a vivid 3D topol. pattern and the vector gradient field of
which is detd. by the electron transition c.d. A primary goal is to interpret
the "anomalous" strength of the intramol. hydrogen bond O-H···X
formed in cis ortho-X substituted phenols, depending upon the halogen atom (X =
F, Cl, and Br) in terms of the populations of the electronic localization
function basins and a so-called core valence bifurcation index. A theor. model
is considered aiming to explain convincingly the cis-trans conversion in
ortho-X phenols occurring in some solvents and resulting in the exptl. obsd.
splitting of the νOH stretch and based on the Pauling model. Characteristic
harmonic vibrational modes of all monohalogen substituted phenols are discussed
thoroughly. The order of stability of monohalogen substituted phenols is
established at a high level of computational performance, showing the
"anomalous" order of stability of fluorophenols, the result being
that, in contrast to Cl and Br, the F atom favors the trans meta position over
the cis ortho with formation of the intramol. hydrogen bond.
13- F. Ample, D.
Currulla, F. Fuster, A. Clotet and J. M. Ricart, "Adsorption of CO and CN-
on transition metal surfaces: a comparative study of the bonding
mechanism", Surface Science (2002), 497(1-3), 139-154.
A comparative study of the chemisorption of
the isoelectronic species CO and CN- on Rh, Ni, Pd and Pt(1 1 1) surfaces was
performed using the cluster model approach and the d. functional theory. The CO
bond is weakened whereas the CN- one is strengthened upon chemisorption in
agreement with exptl. evidence based on shifts to lower or higher frequencies,
resp., with respect the vibrational frequency of the free adsorbate. The
details of the chemisorption bond were studied using different techniques
including a topol. anal. of the electron localization function and the
projection orbitals method. A correlation between the substrate-adsorbate
charge transfer and the frequency shift was found.
12- H.
Chevreau, F. Fuster et B. Silvi, “Chemical bond: myth or reality? topological
methods of bond description. Théorie topologique de la liaison
chimique : le Lewis moderne ", L'actualité Chimique,
Société Française de Chimie (2001), (3), 15-22.
Version électronique ici
The vocabulary and majority of the concepts
used to describe bonds in mols. and solids were introduced at the beginning of
the XXth century by Lewis. The topol. anal. of the ELF function, presented in
the first part, is a math. vision of the Lewis theory. This method gives
access to a partition of mol. space into regions which have a clear chem.
sense. In the second time, various examples extd. from the org. chem., chem.-physics
and solid state chem., illustrate the contribution of this theory to the chem.
bond knowledge.
11- R. Llusar, A.
Beltran, J. Andrés, F. Fuster and B. Silvi, " Topological Analysis of
Multiple Metal-Metal Bonds in Dimers of the M2(Formamidinate)4
Type with M= Nb, Mo, Tc, Ru, Rh and Pd", Journal of Physical
Chemistry A,105, 9460-9466 (2001).
The chem. bond in complexes of the
M2(formamidinate)4 type with different nominal bond orders has been
investigated within the framework of the present topol. theories. The
atoms-in-mols. (AIM) anal. of the theor. calcd. electron d. shows low ρ(r)
values at the metal-metal bond crit. point (rc), which makes difficult a topol.
description of the interaction using the electron d. as the scalar function. When
the electron localization function (ELF) is used instead, four disynaptic
metal-metal valence basins, V(M,M), are found for the Mo and Nb dimers, one for
each the Ru and Rh complexes, while no disynaptic basins are obtained for the
Tc and Pd systems. The V(M,M) basins are not the dominant features of the
interaction due to their low population values with the main contribution
arising from the "4d" metal electrons. However, the MOs involving
the "4d" function of the metal essentially contribute to the metal core
basins, C(M). The most important characteristic of the metal-metal bond is the
abnormally high values for the metal-metal core covariance, B(M,M), and the AIM
at. basins covariances, λc(ρ). This large electron fluctuation which
occurs between the two metallic cores is interpreted in terms of simple
resonance arguments. Except for Rh, there is an excellent correlation between
the core covariances, B(M,M), and the metal-metal distances.
10- F. Fuster, B.
Silvi, S. Berski et Z. Latajka, " Topological aspects of protonation and
hydrogen bonding: the dihydrogen bond case", Journal of Molecular
Structure, 555, 75-84 (2000).
The topol. theory of the chem. bond
suggests that the favored protonation site of a mol. satisfies a least topol.
change principle. This generally means that the nos. of basins in the neutral
and protonated species are equal. If the mol. has one or more lone pair the
protonation takes place in a mono-synaptic basin yielding the formation of a
covalent bond B-H. This process is named covalent protonation accordingly. In
the case of hydrides, MHn, the conservation of the no. of basins implies the
formation of a complex involving MHn-1+ and H2. It is proposed to
name this process as predissociative protonation. The conventional hydrogen
bond A-H···B can be considered as the initial step of a proton transfer
reaction leading to the covalent protonation BH+, whereas the dihydrogen bond,
A-H···H-M, corresponds to the predissociative protonation. This hypothesis has
been investigated on systems involving LiH, BeH2, BH3, CH4
and BH3NH3 as proton acceptor.
9- F. Fuster, A.
Sevin et B. Silvi, "Determination of substitutional sites in heterocycles
from the topological analysis of the electron localization function
(ELF)", Journal of Computational Chemistry, 21, 509-514 (2000).
Topol. anal. of the electron-localization
function (ELF) was carried out on 5-membered (C4H4NH, C4H4PH, C4H4O, C4H4S) and
6-membered (C5H5N, C5H5P) heterocycles. The bonding in these mols. is discussed
on the basis of the valence basin populations. The ELF values at the (3, 1)
crit. points between disynaptic basins related to a given center provide a
criterion to det. substitutional sites.
8- F. Fuster, A.
Sevin et B. Silvi, "Topological analysis of the electron localization
function (ELF) applied to the electrophilic aromatic substitution", Journal
of Physical Chemistry A, 104 (4), 852-858 (2000).
The topol. anal. of the electron
localization function ELF provides a partition of the mol. space into basins of
attractors which have a clear chem. signification. The hierarchy of these
basins is given by the bifurcation of the localization domains. In the case of
π-donor substituents (OH, NH2, F, CH3, C6H5, Cl), the arom. domain is
first opened close to the substituted carbon and then in the vicinity of the
meta carbon; whereas for attractor substituents (CN, CHO, NO2, CF3 and CCl3),
it is first opened in the ortho and para positions. The orienting effects of
the electrophilic substitutions are correlated with these bifurcations. The
exptl. favored positions always correspond to the locally electroneg. carbons
(i.e., those which keep their shell structure at the higher ELF values). This
suggests that the local Pauli repulsion plays a noticeable role in the
orienting effects which are complementary to the charge transfer effect
involved in std. quantum chem. pictures.
7- F. Fuster et B.
Silvi, "Determination of proton sites in bases from topological
rules.", Chemical Physics, 252, 279-287 (2000).
The topol. anal. of the electron
localization function ELF was carried out on neutral and protonated bases
revealing that the detn. of the most favorable protonation site can be done
with the help of a simple rule. The protonation occurs in the most populated valence
basin of the base which yields the least topol. change of the localization
gradient field. This can be viewed as resulting of a competition between the
Pauli repulsion and the stabilization brought by the proton. Structural
comparisons of H bonded complexes and protonated bases are consistent with a
picture in which the formation of the complex is the initial step of the proton
transfer reaction B+HX→ BH++X-. The angular structure of the complex is
such as the proton transfer reaction satisfies the least motion principle of
Rice and Teller. This description brings support to the model of Legon and
Millen which generalizes the VSEPR concepts to H bonded complexes B···HX in
assuming that the H bond is directed towards the nucleophilic center of the basis,
in other words towards the protonation site.
6- F. Fuster et B.
Silvi , " Does Topological approach characterize the hydrogen bond
? ", Theoretical Chemistry Accounts, , 104 (1), 13-21 (2000).
The topol. anal. of the electron
localization function has been applied to complexes representative of the weak,
medium and strong hydrogen bond. For both the weak and the medium hydrogen
bonds, the no. of basins in the complexes is the sum of those of the moieties.
In this case, the formation of a weak or a medium hydrogen-bonded complex does
not involve a chem. reaction. In the weak hydrogen bond case, the redn. of the
localization domain yields two domains in the first step, which can be
partitioned afterwards into valence and core domains. In contrast, for medium
complexes the core-valence sepn. is the first event which occurs during the
redn. process and therefore the complex should be considered as a single mol.
species. Moreover, the anal. of the basin population variance indicates in
this case a noticeable delocalization between the V(A, H) and V(B) basins.
Finally, the sym. strong hydrogen bond has a protonated basin V(H) at the bond
midpoint. Such a topol. corresponds to an incomplete proton transfer and to a
rather covalent bond.
5- J. Bergés, F.
Fuster, J.-P. Jacquot, B. Silvi et C. Houée-Levin " Influence of
protonation on the stability of disulfide radicals ", Intenational
Journal of Nuclear Research (Nukleonika) (2000), 45(1), 23-29.
The ease of disulfide bond cleavage in
peptides and proteins is evaluated by an exptl. method (one-electron redn. by
COO.bul.- radicals and measurement of the chain length) and two theor.
approaches based on quantum chem. and topol. All results show acid-catalysis
of this bond opening. The disulfide bond in the radical state is weakened by
protonation.
4- S. Noury, X.
Krokidis, F. Fuster et B. Silvi, "Computational tools for the electron
localization function topological analysis", Computer and Chemistry,
23(6), 597-604 (1999).
The algorithms used to generate three-dimensional
grids of the electron localization function ELF, to assign the data points to
basins, and to perform the integration of the one-electron d. and of the pair
functions over the basins are described. These algorithms take advantage of
the factorization of the Cartesian Gaussian functions which enables to compute
heavy CPU-consuming intermediates in external short loops. The performances of
these algorithm, i.e., speed vs. accuracy are discussed.
3- L. Joubert, B.
Silvi, G. Picard et F. Fuster, " Topological analysis of the Electron
Localization Function : a help for understanding the complex structure of
cryolitic melts " Journal of the Electrochemical Society, 146
(6), 2180-2183 (1999).
A theor. study of the solvated AlF63-,
AlF52-, and AlF4- species which are involved in cryolitic melts was performed.
Based on the d. functional theory formalism, a structural and vibrational anal.
of these isolated mols. was carried out, allowing detn. of their relative
stabilities. A further topol. anal. of the electron localization function
gradient field reveals this to be a powerful tool to provide insight into the
bonding properties of these mols. The dative-polarized character of these
species was characterized, and the structural effect of the calcium
countercation was investigated.
2- L. Joubert, G.
Picard, B. Silvi et F. Fuster, " Electron Localization Function view
of bonding in selected Aluminium Fluoride molecules. ", Journal of
Molecular Structure (Theochem), 463 (1-2), 75-80 (1999).
A series of calcns. has been performed on
AlF4- and CaAlF5 species in order to refine their equil. geometries as well as
to get some insight onto their bonding properties. These species play an
important role in electrochem. industrial processes such as the electrowinning
of aluminum (i.e. the Heroult-Hall process). The calcns. have been performed
within the d. functional approach using the B3LYP hybrid functional and the
6-311 + +G(3df,2p) all-electron basis sets on all the at. centers. The
optimized geometries and the calcd. frequencies of AlF4- are found to be in
agreement with those previously obtained at a lower level of calcn. and with
expts. The bonding has been investigated by the topol. anal. of the electron
localization function gradient field. The anal. indicates that the Al-F bond
presents a noticeable covalent character confirmed by the presence of a
disynaptic basin between the Al and F cores. The basins' populations and their
fluctuations have been calcd. indicating an important delocalization between
the Al-F bond and the fluorine's lone pairs. Moreover, the structural role of
the counter cation Ca2+ has been emphasized. A structural and topol. anal. of
CaAlF5 has been carried out. This study has clearly established the purely
ionic interaction between F-, AlF3 and Ca2+ fragments in CaAlF5 mol.
1- F.
Fuster, B. Silvi, G. Picard et L. Joubert, " ELF characterization of
iono-covalent Bondings in Aluminium(III) chloride-fluoride
complexes ", Light Metals 1998, édité par B. Welch, (Metals &
Marerails Society, Warrendale, PA :The Minerals), 555-558.
A conformational study of the complex
species relevant to the industrial electrorefining process of aluminum has been
performed. The four-fold coordinated aluminum(III) complexes involving
chloride and fluoride anions have been investigated. Each bond of
aluminum(III) with a particular chloride or fluoride anion has been
characterized using the topol. anal. of the Electron Localization Function
(ELF) gradient field. This theor. approach has been used to interpret the
relative stabilities of these complexes.